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root/OpenMD/branches/development/src/brains/SimCreator.cpp

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trunk/src/brains/SimCreator.cpp (file contents), Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file SimCreator.cpp
45		* @author tlin
46		* @date 11/03/2004
46	–	* @time 13:51am
47		* @version 1.0
48		*/
49	+	#include <exception>
50	+	#include <iostream>
51	+	#include <sstream>
52	+	#include <string>
53
50	–	#include <sprng.h>
51	–
54		#include "brains/MoleculeCreator.hpp"
55		#include "brains/SimCreator.hpp"
56		#include "brains/SimSnapshotManager.hpp"
57		#include "io/DumpReader.hpp"
58	<	#include "io/parse_me.h"
57	<	#include "UseTheForce/ForceFieldFactory.hpp"
58	>	#include "brains/ForceField.hpp"
59		#include "utils/simError.h"
60		#include "utils/StringUtils.hpp"
61	<	#ifdef IS_MPI
62	<	#include "io/mpiBASS.h"
63	<	#include "math/randomSPRNG.hpp"
64	<	#endif
61	>	#include "math/SeqRandNumGen.hpp"
62	>	#include "mdParser/MDLexer.hpp"
63	>	#include "mdParser/MDParser.hpp"
64	>	#include "mdParser/MDTreeParser.hpp"
65	>	#include "mdParser/SimplePreprocessor.hpp"
66	>	#include "antlr/ANTLRException.hpp"
67	>	#include "antlr/TokenStreamRecognitionException.hpp"
68	>	#include "antlr/TokenStreamIOException.hpp"
69	>	#include "antlr/TokenStreamException.hpp"
70	>	#include "antlr/RecognitionException.hpp"
71	>	#include "antlr/CharStreamException.hpp"
72
73	<	namespace oopse {
73	>	#include "antlr/MismatchedCharException.hpp"
74	>	#include "antlr/MismatchedTokenException.hpp"
75	>	#include "antlr/NoViableAltForCharException.hpp"
76	>	#include "antlr/NoViableAltException.hpp"
77
78	<	void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
78	>	#include "types/DirectionalAdapter.hpp"
79	>	#include "types/MultipoleAdapter.hpp"
80	>	#include "types/EAMAdapter.hpp"
81	>	#include "types/SuttonChenAdapter.hpp"
82	>	#include "types/PolarizableAdapter.hpp"
83	>	#include "types/FixedChargeAdapter.hpp"
84	>	#include "types/FluctuatingChargeAdapter.hpp"
85
86		#ifdef IS_MPI
87	+	#include "mpi.h"
88	+	#include "math/ParallelRandNumGen.hpp"
89	+	#endif
90
91	<	if (worldRank == 0) {
92	<	#endif // is_mpi
91	>	namespace OpenMD {
92	>
93	>	Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){
94	>	Globals* simParams = NULL;
95	>	try {
96
97	<	simParams->initalize();
98	<	set_interface_stamps(stamps, simParams);
97	>	// Create a preprocessor that preprocesses md file into an ostringstream
98	>	std::stringstream ppStream;
99	>	#ifdef IS_MPI
100	>	int streamSize;
101	>	const int masterNode = 0;
102	>	int commStatus;
103	>	if (worldRank == masterNode) {
104	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
105	>	#endif
106	>	SimplePreprocessor preprocessor;
107	>	preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
108	>
109	>	#ifdef IS_MPI
110	>	//brocasting the stream size
111	>	streamSize = ppStream.str().size() +1;
112	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
113
114	<	#ifdef IS_MPI
114	>	commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
115	>
116	>
117	>	} else {
118
119	<	mpiEventInit();
119	>	commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
120
121	<	#endif
121	>	//get stream size
122	>	commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
123
124	<	yacc_BASS(mdFileName.c_str());
124	>	char* buf = new char[streamSize];
125	>	assert(buf);
126	>
127	>	//receive file content
128	>	commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
129	>
130	>	ppStream.str(buf);
131	>	delete [] buf;
132
133	<	#ifdef IS_MPI
133	>	}
134	>	#endif
135	>	// Create a scanner that reads from the input stream
136	>	MDLexer lexer(ppStream);
137	>	lexer.setFilename(filename);
138	>	lexer.initDeferredLineCount();
139	>
140	>	// Create a parser that reads from the scanner
141	>	MDParser parser(lexer);
142	>	parser.setFilename(filename);
143
144	<	throwMPIEvent(NULL);
145	<	} else {
146	<	set_interface_stamps(stamps, simParams);
147	<	mpiEventInit();
148	<	MPIcheckPoint();
149	<	mpiEventLoop();
144	>	// Create an observer that synchorizes file name change
145	>	FilenameObserver observer;
146	>	observer.setLexer(&lexer);
147	>	observer.setParser(&parser);
148	>	lexer.setObserver(&observer);
149	>
150	>	antlr::ASTFactory factory;
151	>	parser.initializeASTFactory(factory);
152	>	parser.setASTFactory(&factory);
153	>	parser.mdfile();
154	>
155	>	// Create a tree parser that reads information into Globals
156	>	MDTreeParser treeParser;
157	>	treeParser.initializeASTFactory(factory);
158	>	treeParser.setASTFactory(&factory);
159	>	simParams = treeParser.walkTree(parser.getAST());
160		}
161
162	<	#endif
162	>
163	>	catch(antlr::MismatchedCharException& e) {
164	>	sprintf(painCave.errMsg,
165	>	"parser exception: %s %s:%d:%d\n",
166	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
167	>	painCave.isFatal = 1;
168	>	simError();
169	>	}
170	>	catch(antlr::MismatchedTokenException &e) {
171	>	sprintf(painCave.errMsg,
172	>	"parser exception: %s %s:%d:%d\n",
173	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	catch(antlr::NoViableAltForCharException &e) {
178	>	sprintf(painCave.errMsg,
179	>	"parser exception: %s %s:%d:%d\n",
180	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184	>	catch(antlr::NoViableAltException &e) {
185	>	sprintf(painCave.errMsg,
186	>	"parser exception: %s %s:%d:%d\n",
187	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
188	>	painCave.isFatal = 1;
189	>	simError();
190	>	}
191	>
192	>	catch(antlr::TokenStreamRecognitionException& e) {
193	>	sprintf(painCave.errMsg,
194	>	"parser exception: %s %s:%d:%d\n",
195	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199	>
200	>	catch(antlr::TokenStreamIOException& e) {
201	>	sprintf(painCave.errMsg,
202	>	"parser exception: %s\n",
203	>	e.getMessage().c_str());
204	>	painCave.isFatal = 1;
205	>	simError();
206	>	}
207	>
208	>	catch(antlr::TokenStreamException& e) {
209	>	sprintf(painCave.errMsg,
210	>	"parser exception: %s\n",
211	>	e.getMessage().c_str());
212	>	painCave.isFatal = 1;
213	>	simError();
214	>	}
215	>	catch (antlr::RecognitionException& e) {
216	>	sprintf(painCave.errMsg,
217	>	"parser exception: %s %s:%d:%d\n",
218	>	e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222	>	catch (antlr::CharStreamException& e) {
223	>	sprintf(painCave.errMsg,
224	>	"parser exception: %s\n",
225	>	e.getMessage().c_str());
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	catch (OpenMDException& e) {
230	>	sprintf(painCave.errMsg,
231	>	"%s\n",
232	>	e.getMessage().c_str());
233	>	painCave.isFatal = 1;
234	>	simError();
235	>	}
236	>	catch (std::exception& e) {
237	>	sprintf(painCave.errMsg,
238	>	"parser exception: %s\n",
239	>	e.what());
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243
244	<	}
245	<
246	<	SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
244	>	simParams->setMDfileVersion(mdFileVersion);
245	>	return simParams;
246	>	}
247	>
248	>	SimInfo*  SimCreator::createSim(const std::string & mdFileName,
249	>	bool loadInitCoords) {
250
251	<	MakeStamps * stamps = new MakeStamps();
251	>	const int bufferSize = 65535;
252	>	char buffer[bufferSize];
253	>	int lineNo = 0;
254	>	std::string mdRawData;
255	>	int metaDataBlockStart = -1;
256	>	int metaDataBlockEnd = -1;
257	>	int i;
258	>	streamoff mdOffset;
259	>	int mdFileVersion;
260
103	–	Globals * simParams = new Globals();
261
262	<	//parse meta-data file
263	<	parseFile(mdFileName, stamps, simParams);
262	>	#ifdef IS_MPI
263	>	const int masterNode = 0;
264	>	if (worldRank == masterNode) {
265	>	#endif
266
267	<	//create the force field
268	<	ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
269	<	simParams->getForceField());
270	<
271	<	if (ff == NULL) {
272	<	sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
273	<	simParams->getForceField());
274	<	painCave.isFatal = 1;
275	<	simError();
267	>	std::ifstream mdFile_;
268	>	mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary);
269	>
270	>	if (mdFile_.fail()) {
271	>	sprintf(painCave.errMsg,
272	>	"SimCreator: Cannot open file: %s\n",
273	>	mdFileName.c_str());
274	>	painCave.isFatal = 1;
275	>	simError();
276	>	}
277	>
278	>	mdFile_.getline(buffer, bufferSize);
279	>	++lineNo;
280	>	std::string line = trimLeftCopy(buffer);
281	>	i = CaseInsensitiveFind(line, "<OpenMD");
282	>	if (static_cast<size_t>(i) == string::npos) {
283	>	// try the older file strings to see if that works:
284	>	i = CaseInsensitiveFind(line, "<OOPSE");
285	>	}
286	>
287	>	if (static_cast<size_t>(i) == string::npos) {
288	>	// still no luck!
289	>	sprintf(painCave.errMsg,
290	>	"SimCreator: File: %s is not a valid OpenMD file!\n",
291	>	mdFileName.c_str());
292	>	painCave.isFatal = 1;
293	>	simError();
294	>	}
295	>
296	>	// found the correct opening string, now try to get the file
297	>	// format version number.
298	>
299	>	StringTokenizer tokenizer(line, "=<> \t\n\r");
300	>	std::string fileType = tokenizer.nextToken();
301	>	toUpper(fileType);
302	>
303	>	mdFileVersion = 0;
304	>
305	>	if (fileType == "OPENMD") {
306	>	while (tokenizer.hasMoreTokens()) {
307	>	std::string token(tokenizer.nextToken());
308	>	toUpper(token);
309	>	if (token == "VERSION") {
310	>	mdFileVersion = tokenizer.nextTokenAsInt();
311	>	break;
312	>	}
313	>	}
314	>	}
315	>
316	>	//scan through the input stream and find MetaData tag
317	>	while(mdFile_.getline(buffer, bufferSize)) {
318	>	++lineNo;
319	>
320	>	std::string line = trimLeftCopy(buffer);
321	>	if (metaDataBlockStart == -1) {
322	>	i = CaseInsensitiveFind(line, "<MetaData>");
323	>	if (i != string::npos) {
324	>	metaDataBlockStart = lineNo;
325	>	mdOffset = mdFile_.tellg();
326	>	}
327	>	} else {
328	>	i = CaseInsensitiveFind(line, "</MetaData>");
329	>	if (i != string::npos) {
330	>	metaDataBlockEnd = lineNo;
331	>	}
332	>	}
333	>	}
334	>
335	>	if (metaDataBlockStart == -1) {
336	>	sprintf(painCave.errMsg,
337	>	"SimCreator: File: %s did not contain a <MetaData> tag!\n",
338	>	mdFileName.c_str());
339	>	painCave.isFatal = 1;
340	>	simError();
341	>	}
342	>	if (metaDataBlockEnd == -1) {
343	>	sprintf(painCave.errMsg,
344	>	"SimCreator: File: %s did not contain a closed MetaData block!\n",
345	>	mdFileName.c_str());
346	>	painCave.isFatal = 1;
347	>	simError();
348	>	}
349	>
350	>	mdFile_.clear();
351	>	mdFile_.seekg(0);
352	>	mdFile_.seekg(mdOffset);
353	>
354	>	mdRawData.clear();
355	>
356	>	for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
357	>	mdFile_.getline(buffer, bufferSize);
358	>	mdRawData += buffer;
359	>	mdRawData += "\n";
360	>	}
361	>
362	>	mdFile_.close();
363	>
364	>	#ifdef IS_MPI
365		}
366	+	#endif
367
368	+	std::stringstream rawMetaDataStream(mdRawData);
369	+
370	+	//parse meta-data file
371	+	Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion,
372	+	metaDataBlockStart + 1);
373	+
374	+	//create the force field
375	+	ForceField * ff = new ForceField(simParams->getForceField());
376	+
377	+	if (ff == NULL) {
378	+	sprintf(painCave.errMsg,
379	+	"ForceField Factory can not create %s force field\n",
380	+	simParams->getForceField().c_str());
381	+	painCave.isFatal = 1;
382	+	simError();
383	+	}
384	+
385		if (simParams->haveForceFieldFileName()) {
386	<	ff->setForceFieldFileName(simParams->getForceFieldFileName());
386	>	ff->setForceFieldFileName(simParams->getForceFieldFileName());
387		}
388
389		std::string forcefieldFileName;
390		forcefieldFileName = ff->getForceFieldFileName();
391	<
391	>
392		if (simParams->haveForceFieldVariant()) {
393	<	//If the force field has variant, the variant force field name will be
394	<	//Base.variant.frc. For exampel EAM.u6.frc
395	<
396	<	std::string variant = simParams->getForceFieldVariant();
397	<
398	<	std::string::size_type pos = forcefieldFileName.rfind(".frc");
399	<	variant = "." + variant;
400	<	if (pos != std::string::npos) {
401	<	forcefieldFileName.insert(pos, variant);
402	<	} else {
403	<	//If the default force field file name does not containt .frc suffix, just append the .variant
404	<	forcefieldFileName.append(variant);
405	<	}
393	>	//If the force field has variant, the variant force field name will be
394	>	//Base.variant.frc. For exampel EAM.u6.frc
395	>
396	>	std::string variant = simParams->getForceFieldVariant();
397	>
398	>	std::string::size_type pos = forcefieldFileName.rfind(".frc");
399	>	variant = "." + variant;
400	>	if (pos != std::string::npos) {
401	>	forcefieldFileName.insert(pos, variant);
402	>	} else {
403	>	//If the default force field file name does not containt .frc suffix, just append the .variant
404	>	forcefieldFileName.append(variant);
405	>	}
406		}
407
408		ff->parse(forcefieldFileName);
143	–
144	–	//extract the molecule stamps
145	–	std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
146	–	compList(stamps, simParams, moleculeStampPairs);
147	–
409		//create SimInfo
410	<	SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
410	>	SimInfo * info = new SimInfo(ff, simParams);
411
412	<	//gather parameters (SimCreator only retrieves part of the parameters)
412	>	info->setRawMetaData(mdRawData);
413	>
414	>	//gather parameters (SimCreator only retrieves part of the
415	>	//parameters)
416		gatherParameters(info, mdFileName);
417	<
417	>
418		//divide the molecules and determine the global index of molecules
419		#ifdef IS_MPI
420		divideMolecules(info);
421		#endif
422	<
422	>
423		//create the molecules
424		createMolecules(info);
425	+
426	+	//find the storage layout
427
428	+	int storageLayout = computeStorageLayout(info);
429
430	<	//allocate memory for DataStorage(circular reference, need to break it)
431	<	info->setSnapshotManager(new SimSnapshotManager(info));
430	>	//allocate memory for DataStorage(circular reference, need to
431	>	//break it)
432	>	info->setSnapshotManager(new SimSnapshotManager(info, storageLayout));
433
434	<	//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
435	<	//global index will never change again). Local indices of atoms and rigidbodies are already set by
436	<	//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
434	>	//set the global index of atoms, rigidbodies and cutoffgroups
435	>	//(only need to be set once, the global index will never change
436	>	//again). Local indices of atoms and rigidbodies are already set
437	>	//by MoleculeCreator class which actually delegates the
438	>	//responsibility to LocalIndexManager.
439		setGlobalIndex(info);
440	<
441	<	//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
442	<	//atoms don't have the global index yet  (their global index are all initialized to -1).
443	<	//Therefore we have to call addExcludePairs explicitly here. A way to work around is that
444	<	//we can determine the beginning global indices of atoms before they get created.
440	>
441	>	//Although addInteractionPairs is called inside SimInfo's addMolecule
442	>	//method, at that point atoms don't have the global index yet
443	>	//(their global index are all initialized to -1).  Therefore we
444	>	//have to call addInteractionPairs explicitly here. A way to work
445	>	//around is that we can determine the beginning global indices of
446	>	//atoms before they get created.
447		SimInfo::MoleculeIterator mi;
448		Molecule* mol;
449		for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
450	<	info->addExcludePairs(mol);
450	>	info->addInteractionPairs(mol);
451		}
452
181	–
182	–	//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183	–	//eta, chi for NPT integrator)
453		if (loadInitCoords)
454	<	loadCoordinates(info);
186	<
454	>	loadCoordinates(info, mdFileName);
455		return info;
456	<	}
457	<
458	<	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
459	<
460	<	//setup seed for random number generator
193	<	int seedValue;
194	<	Globals * simParams = info->getSimParams();
195	<
196	<	if (simParams->haveSeed()) {
197	<	seedValue = simParams->getSeed();
198	<
199	<	if (seedValue < 100000000 ) {
200	<	sprintf(painCave.errMsg,
201	<	"Seed for sprng library should contain at least 9 digits\n"
202	<	"OOPSE will generate a seed for user\n");
203	<
204	<	painCave.isFatal = 0;
205	<	simError();
206	<
207	<	//using seed generated by system instead of invalid seed set by user
208	<
209	<	#ifndef IS_MPI
210	<
211	<	seedValue = make_sprng_seed();
212	<
213	<	#else
214	<
215	<	if (worldRank == 0) {
216	<	seedValue = make_sprng_seed();
217	<	}
218	<
219	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
220	<
221	<	#endif
222	<
223	<	} //end if (seedValue /1000000000 == 0)
224	<	} else {
225	<
226	<	#ifndef IS_MPI
227	<
228	<	seedValue = make_sprng_seed();
229	<
230	<	#else
231	<
232	<	if (worldRank == 0) {
233	<	seedValue = make_sprng_seed();
234	<	}
235	<
236	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
237	<
238	<	#endif
239	<
240	<	} //end of simParams->haveSeed()
241	<
242	<	info->setSeed(seedValue);
243	<
244	<
245	<	//figure out the ouput file names
456	>	}
457	>
458	>	void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
459	>
460	>	//figure out the output file names
461		std::string prefix;
462	<
462	>
463		#ifdef IS_MPI
464	<
464	>
465		if (worldRank == 0) {
466		#endif // is_mpi
467	<
468	<	if (simParams->haveFinalConfig()) {
469	<	prefix = getPrefix(simParams->getFinalConfig());
470	<	} else {
471	<	prefix = getPrefix(mdfile);
472	<	}
473	<
474	<	info->setFinalConfigFileName(prefix + ".eor");
475	<	info->setDumpFileName(prefix + ".dump");
476	<	info->setStatFileName(prefix + ".stat");
477	<
467	>	Globals * simParams = info->getSimParams();
468	>	if (simParams->haveFinalConfig()) {
469	>	prefix = getPrefix(simParams->getFinalConfig());
470	>	} else {
471	>	prefix = getPrefix(mdfile);
472	>	}
473	>
474	>	info->setFinalConfigFileName(prefix + ".eor");
475	>	info->setDumpFileName(prefix + ".dump");
476	>	info->setStatFileName(prefix + ".stat");
477	>	info->setRestFileName(prefix + ".zang");
478	>
479		#ifdef IS_MPI
480	<
480	>
481		}
482	<
482	>
483		#endif
484	<
485	<	}
486	<
484	>
485	>	}
486	>
487		#ifdef IS_MPI
488	<	void SimCreator::divideMolecules(SimInfo *info) {
489	<	double numerator;
490	<	double denominator;
491	<	double precast;
492	<	double x;
493	<	double y;
494	<	double a;
488	>	void SimCreator::divideMolecules(SimInfo *info) {
489	>	RealType numerator;
490	>	RealType denominator;
491	>	RealType precast;
492	>	RealType x;
493	>	RealType y;
494	>	RealType a;
495		int old_atoms;
496		int add_atoms;
497		int new_atoms;
#	Line 287 | Line 503 | void SimCreator::divideMolecules(SimInfo *info) {
503		int which_proc;
504		int nProcessors;
505		std::vector<int> atomsPerProc;
290	–	randomSPRNG myRandom(info->getSeed());
506		int nGlobalMols = info->getNGlobalMolecules();
507		std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
508
509	<	MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
510	<
509	>	nProcessors = MPI::COMM_WORLD.Get_size();
510	>
511		if (nProcessors > nGlobalMols) {
512	<	sprintf(painCave.errMsg,
513	<	"nProcessors (%d) > nMol (%d)\n"
514	<	"\tThe number of processors is larger than\n"
515	<	"\tthe number of molecules.  This will not result in a \n"
516	<	"\tusable division of atoms for force decomposition.\n"
517	<	"\tEither try a smaller number of processors, or run the\n"
518	<	"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
519	<
520	<	painCave.isFatal = 1;
521	<	simError();
512	>	sprintf(painCave.errMsg,
513	>	"nProcessors (%d) > nMol (%d)\n"
514	>	"\tThe number of processors is larger than\n"
515	>	"\tthe number of molecules.  This will not result in a \n"
516	>	"\tusable division of atoms for force decomposition.\n"
517	>	"\tEither try a smaller number of processors, or run the\n"
518	>	"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
519	>
520	>	painCave.isFatal = 1;
521	>	simError();
522		}
523	<
523	>
524	>	int seedValue;
525	>	Globals * simParams = info->getSimParams();
526	>	SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator
527	>	if (simParams->haveSeed()) {
528	>	seedValue = simParams->getSeed();
529	>	myRandom = new SeqRandNumGen(seedValue);
530	>	}else {
531	>	myRandom = new SeqRandNumGen();
532	>	}
533	>
534	>
535		a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
536	<
536	>
537		//initialize atomsPerProc
538		atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
539	<
539	>
540		if (worldRank == 0) {
541	<	numerator = info->getNGlobalAtoms();
542	<	denominator = nProcessors;
543	<	precast = numerator / denominator;
544	<	nTarget = (int)(precast + 0.5);
541	>	numerator = info->getNGlobalAtoms();
542	>	denominator = nProcessors;
543	>	precast = numerator / denominator;
544	>	nTarget = (int)(precast + 0.5);
545	>
546	>	for(i = 0; i < nGlobalMols; i++) {
547
548	<	for(i = 0; i < nGlobalMols; i++) {
549	<	done = 0;
550	<	loops = 0;
551	<
552	<	while (!done) {
553	<	loops++;
548	>	done = 0;
549	>	loops = 0;
550	>
551	>	while (!done) {
552	>	loops++;
553	>
554	>	// Pick a processor at random
555	>
556	>	which_proc = (int) (myRandom->rand() * nProcessors);
557	>
558	>	//get the molecule stamp first
559	>	int stampId = info->getMoleculeStampId(i);
560	>	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
561	>
562	>	// How many atoms does this processor have so far?
563	>	old_atoms = atomsPerProc[which_proc];
564	>	add_atoms = moleculeStamp->getNAtoms();
565	>	new_atoms = old_atoms + add_atoms;
566	>
567	>	// If we've been through this loop too many times, we need
568	>	// to just give up and assign the molecule to this processor
569	>	// and be done with it.
570	>
571	>	if (loops > 100) {
572
573	<	// Pick a processor at random
574	<
575	<	which_proc = (int) (myRandom.getRandom() * nProcessors);
576	<
577	<	//get the molecule stamp first
578	<	int stampId = info->getMoleculeStampId(i);
579	<	MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId);
580	<
581	<	// How many atoms does this processor have so far?
582	<	old_atoms = atomsPerProc[which_proc];
583	<	add_atoms = moleculeStamp->getNAtoms();
584	<	new_atoms = old_atoms + add_atoms;
585	<
586	<	// If we've been through this loop too many times, we need
587	<	// to just give up and assign the molecule to this processor
588	<	// and be done with it.
589	<
590	<	if (loops > 100) {
591	<	sprintf(painCave.errMsg,
592	<	"I've tried 100 times to assign molecule %d to a "
593	<	" processor, but can't find a good spot.\n"
594	<	"I'm assigning it at random to processor %d.\n",
595	<	i, which_proc);
596	<
597	<	painCave.isFatal = 0;
598	<	simError();
599	<
600	<	molToProcMap[i] = which_proc;
601	<	atomsPerProc[which_proc] += add_atoms;
602	<
603	<	done = 1;
604	<	continue;
605	<	}
606	<
607	<	// If we can add this molecule to this processor without sending
608	<	// it above nTarget, then go ahead and do it:
609	<
610	<	if (new_atoms <= nTarget) {
611	<	molToProcMap[i] = which_proc;
612	<	atomsPerProc[which_proc] += add_atoms;
613	<
614	<	done = 1;
615	<	continue;
616	<	}
617	<
618	<	// The only situation left is when new_atoms > nTarget.  We
619	<	// want to accept this with some probability that dies off the
620	<	// farther we are from nTarget
375	<
376	<	// roughly:  x = new_atoms - nTarget
377	<	//           Pacc(x) = exp(- a * x)
378	<	// where a = penalty / (average atoms per molecule)
379	<
380	<	x = (double)(new_atoms - nTarget);
381	<	y = myRandom.getRandom();
382	<
383	<	if (y < exp(- a * x)) {
384	<	molToProcMap[i] = which_proc;
385	<	atomsPerProc[which_proc] += add_atoms;
386	<
387	<	done = 1;
388	<	continue;
389	<	} else {
390	<	continue;
391	<	}
392	<	}
573	>	sprintf(painCave.errMsg,
574	>	"There have been 100 attempts to assign molecule %d to an\n"
575	>	"\tunderworked processor, but there's no good place to\n"
576	>	"\tleave it.  OpenMD is assigning it at random to processor %d.\n",
577	>	i, which_proc);
578	>
579	>	painCave.isFatal = 0;
580	>	painCave.severity = OPENMD_INFO;
581	>	simError();
582	>
583	>	molToProcMap[i] = which_proc;
584	>	atomsPerProc[which_proc] += add_atoms;
585	>
586	>	done = 1;
587	>	continue;
588	>	}
589	>
590	>	// If we can add this molecule to this processor without sending
591	>	// it above nTarget, then go ahead and do it:
592	>
593	>	if (new_atoms <= nTarget) {
594	>	molToProcMap[i] = which_proc;
595	>	atomsPerProc[which_proc] += add_atoms;
596	>
597	>	done = 1;
598	>	continue;
599	>	}
600	>
601	>	// The only situation left is when new_atoms > nTarget.  We
602	>	// want to accept this with some probability that dies off the
603	>	// farther we are from nTarget
604	>
605	>	// roughly:  x = new_atoms - nTarget
606	>	//           Pacc(x) = exp(- a * x)
607	>	// where a = penalty / (average atoms per molecule)
608	>
609	>	x = (RealType)(new_atoms - nTarget);
610	>	y = myRandom->rand();
611	>
612	>	if (y < exp(- a * x)) {
613	>	molToProcMap[i] = which_proc;
614	>	atomsPerProc[which_proc] += add_atoms;
615	>
616	>	done = 1;
617	>	continue;
618	>	} else {
619	>	continue;
620	>	}
621		}
622	+	}
623	+
624	+	delete myRandom;
625
626	<	// Spray out this nonsense to all other processors:
627	<
397	<	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
626	>	// Spray out this nonsense to all other processors:
627	>	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
628		} else {
629	+
630	+	// Listen to your marching orders from processor 0:
631	+	MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
632
400	–	// Listen to your marching orders from processor 0:
401	–
402	–	MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
633		}
634	<
634	>
635		info->setMolToProcMap(molToProcMap);
636		sprintf(checkPointMsg,
637		"Successfully divided the molecules among the processors.\n");
638	<	MPIcheckPoint();
639	<	}
640	<
638	>	errorCheckPoint();
639	>	}
640	>
641		#endif
642	<
643	<	void SimCreator::createMolecules(SimInfo *info) {
642	>
643	>	void SimCreator::createMolecules(SimInfo *info) {
644		MoleculeCreator molCreator;
645		int stampId;
646	<
646	>
647		for(int i = 0; i < info->getNGlobalMolecules(); i++) {
648	<
648	>
649		#ifdef IS_MPI
650	<
651	<	if (info->getMolToProc(i) == worldRank) {
650	>
651	>	if (info->getMolToProc(i) == worldRank) {
652		#endif
653	<
654	<	stampId = info->getMoleculeStampId(i);
655	<	Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
656	<	stampId, i, info->getLocalIndexManager());
657	<
658	<	info->addMolecule(mol);
659	<
653	>
654	>	stampId = info->getMoleculeStampId(i);
655	>	Molecule * mol = molCreator.createMolecule(info->getForceField(),
656	>	info->getMoleculeStamp(stampId),
657	>	stampId, i,
658	>	info->getLocalIndexManager());
659	>
660	>	info->addMolecule(mol);
661	>
662		#ifdef IS_MPI
663	<
664	<	}
665	<
663	>
664	>	}
665	>
666		#endif
667	<
667	>
668		} //end for(int i=0)
669	<	}
669	>	}
670	>
671	>	int SimCreator::computeStorageLayout(SimInfo* info) {
672
673	<	void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
674	<	std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
675	<	int i;
676	<	char * id;
677	<	MoleculeStamp * currentStamp;
678	<	Component** the_components = simParams->getComponents();
679	<	int n_components = simParams->getNComponents();
673	>	Globals* simParams = info->getSimParams();
674	>	int nRigidBodies = info->getNGlobalRigidBodies();
675	>	set<AtomType*> atomTypes = info->getSimulatedAtomTypes();
676	>	set<AtomType*>::iterator i;
677	>	bool hasDirectionalAtoms = false;
678	>	bool hasFixedCharge = false;
679	>	bool hasDipoles = false;
680	>	bool hasQuadrupoles = false;
681	>	bool hasPolarizable = false;
682	>	bool hasFluctuatingCharge = false;
683	>	bool hasMetallic = false;
684	>	int storageLayout = 0;
685	>	storageLayout |= DataStorage::dslPosition;
686	>	storageLayout |= DataStorage::dslVelocity;
687	>	storageLayout |= DataStorage::dslForce;
688
689	<	if (!simParams->haveNMol()) {
448	<	// we don't have the total number of molecules, so we assume it is
449	<	// given in each component
689	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
690
691	<	for(i = 0; i < n_components; i++) {
692	<	if (!the_components[i]->haveNMol()) {
693	<	// we have a problem
694	<	sprintf(painCave.errMsg,
695	<	"SimCreator Error. No global NMol or component NMol given.\n"
696	<	"\tCannot calculate the number of atoms.\n");
691	>	DirectionalAdapter da = DirectionalAdapter( (*i) );
692	>	MultipoleAdapter ma = MultipoleAdapter( (*i) );
693	>	EAMAdapter ea = EAMAdapter( (*i) );
694	>	SuttonChenAdapter sca = SuttonChenAdapter( (*i) );
695	>	PolarizableAdapter pa = PolarizableAdapter( (*i) );
696	>	FixedChargeAdapter fca = FixedChargeAdapter( (*i) );
697	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) );
698
699	<	painCave.isFatal = 1;
700	<	simError();
701	<	}
702	<
703	<	id = the_components[i]->getType();
704	<	currentStamp = (stamps->extractMolStamp(id))->getStamp();
705	<
706	<	if (currentStamp == NULL) {
707	<	sprintf(painCave.errMsg,
708	<	"SimCreator error: Component \"%s\" was not found in the "
709	<	"list of declared molecules\n", id);
710	<
711	<	painCave.isFatal = 1;
712	<	simError();
713	<	}
714	<
715	<	moleculeStampPairs.push_back(
716	<	std::make_pair(currentStamp, the_components[i]->getNMol()));
717	<	} //end for (i = 0; i < n_components; i++)
718	<	} else {
719	<	sprintf(painCave.errMsg, "SimSetup error.\n"
720	<	"\tSorry, the ability to specify total"
721	<	" nMols and then give molfractions in the components\n"
722	<	"\tis not currently supported."
723	<	" Please give nMol in the components.\n");
699	>	if (da.isDirectional()){
700	>	hasDirectionalAtoms = true;
701	>	}
702	>	if (ma.isDipole()){
703	>	hasDipoles = true;
704	>	}
705	>	if (ma.isQuadrupole()){
706	>	hasQuadrupoles = true;
707	>	}
708	>	if (ea.isEAM() || sca.isSuttonChen()){
709	>	hasMetallic = true;
710	>	}
711	>	if ( fca.isFixedCharge() ){
712	>	hasFixedCharge = true;
713	>	}
714	>	if ( fqa.isFluctuatingCharge() ){
715	>	hasFluctuatingCharge = true;
716	>	}
717	>	if ( pa.isPolarizable() ){
718	>	hasPolarizable = true;
719	>	}
720	>	}
721	>
722	>	if (nRigidBodies > 0 || hasDirectionalAtoms) {
723	>	storageLayout |= DataStorage::dslAmat;
724	>	if(storageLayout & DataStorage::dslVelocity) {
725	>	storageLayout |= DataStorage::dslAngularMomentum;
726	>	}
727	>	if (storageLayout & DataStorage::dslForce) {
728	>	storageLayout |= DataStorage::dslTorque;
729	>	}
730	>	}
731	>	if (hasDipoles) {
732	>	storageLayout |= DataStorage::dslDipole;
733	>	}
734	>	if (hasQuadrupoles) {
735	>	storageLayout |= DataStorage::dslQuadrupole;
736	>	}
737	>	if (hasFixedCharge || hasFluctuatingCharge) {
738	>	storageLayout |= DataStorage::dslSkippedCharge;
739	>	}
740	>	if (hasMetallic) {
741	>	storageLayout |= DataStorage::dslDensity;
742	>	storageLayout |= DataStorage::dslFunctional;
743	>	storageLayout |= DataStorage::dslFunctionalDerivative;
744	>	}
745	>	if (hasPolarizable) {
746	>	storageLayout |= DataStorage::dslElectricField;
747	>	}
748	>	if (hasFluctuatingCharge){
749	>	storageLayout |= DataStorage::dslFlucQPosition;
750	>	if(storageLayout & DataStorage::dslVelocity) {
751	>	storageLayout |= DataStorage::dslFlucQVelocity;
752	>	}
753	>	if (storageLayout & DataStorage::dslForce) {
754	>	storageLayout |= DataStorage::dslFlucQForce;
755	>	}
756	>	}
757	>
758	>	// if the user has asked for them, make sure we've got the memory for the
759	>	// objects defined.
760
761	<	painCave.isFatal = 1;
762	<	simError();
761	>	if (simParams->getOutputParticlePotential()) {
762	>	storageLayout |= DataStorage::dslParticlePot;
763		}
764
765	<	#ifdef IS_MPI
765	>	if (simParams->havePrintHeatFlux()) {
766	>	if (simParams->getPrintHeatFlux()) {
767	>	storageLayout |= DataStorage::dslParticlePot;
768	>	}
769	>	}
770
771	<	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
772	<	MPIcheckPoint();
771	>	if (simParams->getOutputElectricField()) {
772	>	storageLayout |= DataStorage::dslElectricField;
773	>	}
774
775	<	#endif // is_mpi
775	>	if (simParams->getOutputFluctuatingCharges()) {
776	>	storageLayout |= DataStorage::dslFlucQPosition;
777	>	storageLayout |= DataStorage::dslFlucQVelocity;
778	>	storageLayout |= DataStorage::dslFlucQForce;
779	>	}
780
781	<	}
781	>	return storageLayout;
782	>	}
783
784	<	void SimCreator::setGlobalIndex(SimInfo *info) {
784	>	void SimCreator::setGlobalIndex(SimInfo *info) {
785		SimInfo::MoleculeIterator mi;
786		Molecule::AtomIterator ai;
787		Molecule::RigidBodyIterator ri;
788		Molecule::CutoffGroupIterator ci;
789	+	Molecule::IntegrableObjectIterator  ioi;
790		Molecule * mol;
791		Atom * atom;
792		RigidBody * rb;
#	Line 507 | Line 795 | void SimCreator::setGlobalIndex(SimInfo *info) {
795		int beginRigidBodyIndex;
796		int beginCutoffGroupIndex;
797		int nGlobalAtoms = info->getNGlobalAtoms();
798	+	int nGlobalRigidBodies = info->getNGlobalRigidBodies();
799
511	–	#ifndef IS_MPI
512	–
800		beginAtomIndex = 0;
801	<	beginRigidBodyIndex = 0;
801	>	//rigidbody's index begins right after atom's
802	>	beginRigidBodyIndex = info->getNGlobalAtoms();
803		beginCutoffGroupIndex = 0;
804
805	<	#else
805	>	for(int i = 0; i < info->getNGlobalMolecules(); i++) {
806	>
807	>	#ifdef IS_MPI
808	>	if (info->getMolToProc(i) == worldRank) {
809	>	#endif
810	>	// stuff to do if I own this molecule
811	>	mol = info->getMoleculeByGlobalIndex(i);
812
519	–	int nproc;
520	–	int myNode;
521	–
522	–	myNode = worldRank;
523	–	MPI_Comm_size(MPI_COMM_WORLD, &nproc);
524	–
525	–	std::vector < int > tmpAtomsInProc(nproc, 0);
526	–	std::vector < int > tmpRigidBodiesInProc(nproc, 0);
527	–	std::vector < int > tmpCutoffGroupsInProc(nproc, 0);
528	–	std::vector < int > NumAtomsInProc(nproc, 0);
529	–	std::vector < int > NumRigidBodiesInProc(nproc, 0);
530	–	std::vector < int > NumCutoffGroupsInProc(nproc, 0);
531	–
532	–	tmpAtomsInProc[myNode] = info->getNAtoms();
533	–	tmpRigidBodiesInProc[myNode] = info->getNRigidBodies();
534	–	tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups();
535	–
536	–	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
537	–	MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,
538	–	MPI_SUM, MPI_COMM_WORLD);
539	–	MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc,
540	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
541	–	MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc,
542	–	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
543	–
544	–	beginAtomIndex = 0;
545	–	beginRigidBodyIndex = 0;
546	–	beginCutoffGroupIndex = 0;
547	–
548	–	for(int i = 0; i < myNode; i++) {
549	–	beginAtomIndex += NumAtomsInProc[i];
550	–	beginRigidBodyIndex += NumRigidBodiesInProc[i];
551	–	beginCutoffGroupIndex += NumCutoffGroupsInProc[i];
552	–	}
553	–
554	–	//rigidbody's index begins right after atom's
555	–	beginRigidBodyIndex += info->getNGlobalAtoms();
556	–	#endif
557	–
558	–	for(mol = info->beginMolecule(mi); mol != NULL;
559	–	mol = info->nextMolecule(mi)) {
560	–
813		//local index(index in DataStorge) of atom is important
814		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
815	<	atom->setGlobalIndex(beginAtomIndex++);
815	>	atom->setGlobalIndex(beginAtomIndex++);
816		}
817	<
817	>
818		for(rb = mol->beginRigidBody(ri); rb != NULL;
819		rb = mol->nextRigidBody(ri)) {
820	<	rb->setGlobalIndex(beginRigidBodyIndex++);
820	>	rb->setGlobalIndex(beginRigidBodyIndex++);
821		}
822	<
823	<	//local index of cutoff group is trivial, it only depends on the order of travesing
822	>
823	>	//local index of cutoff group is trivial, it only depends on
824	>	//the order of travesing
825		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
826		cg = mol->nextCutoffGroup(ci)) {
827	<	cg->setGlobalIndex(beginCutoffGroupIndex++);
828	<	}
829	<	}
827	>	cg->setGlobalIndex(beginCutoffGroupIndex++);
828	>	}
829	>
830	>	#ifdef IS_MPI
831	>	}  else {
832
833	+	// stuff to do if I don't own this molecule
834	+
835	+	int stampId = info->getMoleculeStampId(i);
836	+	MoleculeStamp* stamp = info->getMoleculeStamp(stampId);
837	+
838	+	beginAtomIndex += stamp->getNAtoms();
839	+	beginRigidBodyIndex += stamp->getNRigidBodies();
840	+	beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms();
841	+	}
842	+	#endif
843	+
844	+	} //end for(int i=0)
845	+
846		//fill globalGroupMembership
847		std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0);
848		for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
849	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
850	<
851	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
852	<	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
853	<	}
854	<
855	<	}
849	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
850	>
851	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
852	>	globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex();
853	>	}
854	>
855	>	}
856		}
857	<
857	>
858		#ifdef IS_MPI
859		// Since the globalGroupMembership has been zero filled and we've only
860		// poked values into the atoms we know, we can do an Allreduce
861		// to get the full globalGroupMembership array (We think).
862		// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
863		// docs said we could.
864	<	std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
865	<	MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
866	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
867	<	info->setGlobalGroupMembership(tmpGroupMembership);
864	>	std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
865	>	MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0],
866	>	&tmpGroupMembership[0], nGlobalAtoms,
867	>	MPI::INT, MPI::SUM);
868	>	info->setGlobalGroupMembership(tmpGroupMembership);
869		#else
870		info->setGlobalGroupMembership(globalGroupMembership);
871		#endif
872	<
872	>
873		//fill molMembership
874	<	std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
874	>	std::vector<int> globalMolMembership(info->getNGlobalAtoms() +
875	>	info->getNGlobalRigidBodies(), 0);
876
877	<	for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
878	<
879	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
880	<	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
881	<	}
877	>	for(mol = info->beginMolecule(mi); mol != NULL;
878	>	mol = info->nextMolecule(mi)) {
879	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
880	>	globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
881	>	}
882	>	for (rb = mol->beginRigidBody(ri); rb != NULL;
883	>	rb = mol->nextRigidBody(ri)) {
884	>	globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
885	>	}
886		}
887	<
887	>
888		#ifdef IS_MPI
889	<	std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
890	<
891	<	MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
892	<	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
889	>	std::vector<int> tmpMolMembership(info->getNGlobalAtoms() +
890	>	info->getNGlobalRigidBodies(), 0);
891	>	MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0],
892	>	nGlobalAtoms + nGlobalRigidBodies,
893	>	MPI::INT, MPI::SUM);
894
895		info->setGlobalMolMembership(tmpMolMembership);
896		#else
897		info->setGlobalMolMembership(globalMolMembership);
898		#endif
899
900	<	}
900	>	// nIOPerMol holds the number of integrable objects per molecule
901	>	// here the molecules are listed by their global indices.
902
903	<	void SimCreator::loadCoordinates(SimInfo* info) {
903	>	std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
904	>	for (mol = info->beginMolecule(mi); mol != NULL;
905	>	mol = info->nextMolecule(mi)) {
906	>	nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();
907	>	}
908	>
909	>	#ifdef IS_MPI
910	>	std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
911	>	MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0],
912	>	info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
913	>	#else
914	>	std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
915	>	#endif
916	>
917	>	std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
918	>
919	>	int startingIndex = 0;
920	>	for (int i = 0; i < info->getNGlobalMolecules(); i++) {
921	>	startingIOIndexForMol[i] = startingIndex;
922	>	startingIndex += numIntegrableObjectsPerMol[i];
923	>	}
924	>
925	>	std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
926	>	for (mol = info->beginMolecule(mi); mol != NULL;
927	>	mol = info->nextMolecule(mi)) {
928	>	int myGlobalIndex = mol->getGlobalIndex();
929	>	int globalIO = startingIOIndexForMol[myGlobalIndex];
930	>	for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;
931	>	sd = mol->nextIntegrableObject(ioi)) {
932	>	sd->setGlobalIntegrableObjectIndex(globalIO);
933	>	IOIndexToIntegrableObject[globalIO] = sd;
934	>	globalIO++;
935	>	}
936	>	}
937	>
938	>	info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
939	>
940	>	}
941	>
942	>	void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
943		Globals* simParams;
944	+
945		simParams = info->getSimParams();
946
947	<	if (!simParams->haveInitialConfig()) {
632	<	sprintf(painCave.errMsg,
633	<	"Cannot intialize a simulation without an initial configuration file.\n");
634	<	painCave.isFatal = 1;;
635	<	simError();
636	<	}
637	<
638	<	DumpReader reader(info, simParams->getInitialConfig());
947	>	DumpReader reader(info, mdFileName);
948		int nframes = reader.getNFrames();
949
950		if (nframes > 0) {
951	<	reader.readFrame(nframes - 1);
951	>	reader.readFrame(nframes - 1);
952		} else {
953	<	//invalid initial coordinate file
954	<	sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
955	<	simParams->getInitialConfig());
956	<	painCave.isFatal = 1;
957	<	simError();
953	>	//invalid initial coordinate file
954	>	sprintf(painCave.errMsg,
955	>	"Initial configuration file %s should at least contain one frame\n",
956	>	mdFileName.c_str());
957	>	painCave.isFatal = 1;
958	>	simError();
959		}
650	–
960		//copy the current snapshot to previous snapshot
961		info->getSnapshotManager()->advance();
962	<	}
962	>	}
963	>
964	>	} //end namespace OpenMD
965
655	–	} //end namespace oopse
966
657	–

Comparing:
trunk/src/brains/SimCreator.cpp (property svn:keywords), Revision 285 by tim, Fri Feb 4 05:26:30 2005 UTC vs.
branches/development/src/brains/SimCreator.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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